DOI: 10.18129/B9.bioc.SMITE    

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: Release (3.6)

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

Author: Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally

Maintainer: Neil Ari Wijetunga <Neil.Wijetunga at>, Andrew Damon Johnston <Andrew.Johnston at>

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biocViews Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version 1.6.0
In Bioconductor since BioC 3.3 (R-3.3) (2 years)
License GPL (>=2)
Depends R (>= 3.3), GenomicRanges
Imports scales, plyr, Hmisc, AnnotationDbi,, ggplot2, reactome.db, KEGG.db, BioNet, goseq, methods, IRanges, igraph, Biobase, tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils
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